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# Spectral Tools

Some tools for working with spectral images. Currently these tools are working with channels stored in Z-stacks.

## `channel_plotter.py`

1. Draw an roi on the image
2. Run the script
3. A plot window is displayed next to the image with the average spectrum of the pixels in the roi

Current features:

* The stack position is displayed as red line on the spectrum
* Clicking on the plot will live update image slice position
* Changing image stack position are updated live 
* Chaing the roi will live update the spectrum plot

![](./media/channel_plot.png)

## `slice_max_loc.py`

Performs a Maximum Intensity Projection and records the slice at which the maximum occurs.

It does this by accumulating the MIP as it steps through the stack. At each step if find the pixels on the next slice are more intensity than the current MIP, saves the slice number for these bright pixels to the location image, then updates the MIP.

![](./media/slice_max_loc.png)